Here's what I found, Make sure you don't have a second google-chrome-stable.desktop file in your ~/.local/share/applications folder, for me that fixed the issue by doing:
sudo rm -rf google*.desktop in that folder, the only .desktop files you should have should reside in /usr/share/applications/. Hope this helps.

you can reset unity and compiz by the following commands in the terminal
sudo apt-get install dconf-tools
and then
dconf reset -f /org/compiz/
After that, run the below command to restart Unity
setsid unity
and then to reset the icons use the following code
unity --reset-icons

You cannot move the launcher itself.
Here is the comment on a bug about it
But you can make it look like with Cairo dock.
sudo apt-get install cairo-dock
Now you can play around with configurations and move the dock to the right.
Make Unity's launcher auto-hide and you have a launcher (actually not launcher, it is dock ) on the right.
I like ...

You say you removed the (extra) launchers from ~/.local/usr/share/applications/, but it should be ~/.local/share/applications (without usr).
Remove all google-chrome.desktop files from ~/.local/share/applications and all other .desktop files that may call google-chrome. If you doubt, make the file executable and it will show its icon. Then log out/in.

GNOME commander has a "normal" .desktop file in /usr/share/applications and should be available in Dash.
You probably just need to log out/in to make it available in Dash. Alternatively: run the command
gnome-commander
and lock the icon to the launcher. That will work instantly.

To give you the ability to accept the solution you chose as an answer, I repeat my comment from above. Although it is just a simple workaround and can not really concurrent with @JacobVlijm's impressive answer!
So my hint to you was to just enable the use of different workspaces in your system settings panel. When you have a window opened in one workspace, ...

It's likely you have File Manager running on startup which has a different set of icons in Ubuntu. If you open the app Advanced Settings, and uncheck 'Have file manager handle the desktop' disabled this might help.

Try changing the Launcher Reveal Pressure. The default is 20. You might consider setting it at 1 and systematically try other settings to pick the ideal one.
You can get to this configuration through CCSM (the CompizConfig Settings Manager).
Click on Desktop -> Ubuntu Unity Plugin -> Launcher and change the Launcher Reveal Pressure.
You may have to ...

You can fix this problem partially, like this:
In System Settings, Display, disable one monitor
Start GeoGebra - it will occupy part of your visible screen
Enable the other monitor
Quit GeoGebra
Start GeoGebra with both monitors enabled
You should find it appear within the visible screen.
I have no idea why this works!!!

Using the script below to toggle visibility (with a key combination), you can have one terminal window (completely) hidden when minimized, as if it wouldn't exist, while another terminal window keeps visible in the launcher when minimized.
Create a separate profile for the hidden terminal window
The trick is to create a separate profile in the ...

I used Tilda for this in the past. It has nice feature of showing up and hiding like it's namesake did in Doom or Quake. If you prefer Python version, it's there as well, name's Guake.
It's basically another terminal app, that binds itself to a key combo, and shows only when you press said key combo (hides of course on it as well).
sudo apt-get install ...

There's an option built-in in Ubuntu for doing that, but it looks like it behaves a little buggy: first open the first Terminal (the one you want to be visible) using Ctrl+Alt+T, then open the second Terminal (the one you want to be hidden). While the latter is the active window, hit Ctrl+Alt+S and click elsewhere. To restore it (and here is where I believe ...

The application is definitely running, and probably correctly.
There are a few possibilities:
you have a second screen connected, but it is switched off.
you have workspaces enabled, and Gimp is running on one of your other workspaces / viewports.
In the first case, either disconnect the screen or switch it on to see the application window.
In the ...

Open the shortcut with some text editor like gedit or kate icon by right-clicking on it, and selecting "Open with gedit". In the text editor, shortly after the 'comment' and 'app command' text, you should see something like 'Icon=exec,' (ignore the quotes) change it to Icon=/usr/share/icons/eclipse.png or Icon=eclipse

Some icon conflicts can be resolved by dragging the icons for the programs you need from the /usr/share/applications directory into Docky. Using your file manager, navigate to this folder and give this a try.